library(Seurat)
## Loading required package: ggplot2
## Loading required package: cowplot
## 
## Attaching package: 'cowplot'
## The following object is masked from 'package:ggplot2':
## 
##     ggsave
## Loading required package: Matrix
all10x <- readRDS('/projects/pytrik/sc_adipose/analyze_10x_fluidigm/data/10x')
markers <- read.table('/projects/pytrik/sc_adipose/analyze_10x_fluidigm/data/markergenes/markergenes-cluster12-negbinom.txt', header=T)

Violin plots

VlnPlot(all10x, features.plot=as.vector(markers[,'gene'][1:100]), group.by='res.0.5', point.size.use=-1, nCol=2, x.lab.rot=T, size.x.use=10)

Average expressions

mixcluster_vs_rest <- unlist(lapply(all10x@meta.data$res.0.5, function(x){
  if (x == '12'){
    return('mixcluster')
  } else {
    return('rest')
  }
}))
all10x@meta.data['mixcluster'] <- mixcluster_vs_rest
avg_expr <- AverageExpression(SetAllIdent(all10x, 'mixcluster'), genes.use=as.vector(markers[,'gene'][1:100]))
## Finished averaging RNA for cluster mixcluster
## Finished averaging RNA for cluster rest
print(avg_expr)
##           mixcluster        rest
## RAB13     11.4056217   2.2719939
## DYNC1LI2   2.9724448   0.6170730
## ACTB     107.9807152  28.7649360
## MAP1B     18.5016560   6.5312128
## ANXA2     48.3992075  15.4001891
## LDHA      23.7716134   7.3628231
## SNRPD2     7.6243154   2.6096194
## SKP1      10.8256393   3.7018511
## ATP5B      5.4731719   1.8152643
## PGK1       5.3340770   1.7155981
## PRDX1     14.4368723   4.7837915
## MYL12B    16.5824283   5.6989478
## TPM2      34.4436601  10.3015765
## VDAC1      5.6399890   2.0459610
## NQO1       9.2374137   3.1992011
## LDHB       9.0845190   3.2006484
## PPIA      24.5699183   9.9131921
## MDH1       2.2645885   0.7279586
## ANXA5     13.9581479   5.4019235
## MYL12A    19.3939996   6.9472637
## KIF1C      1.1580022   0.4042845
## ANXA1     11.7331312   4.0801157
## ARF4       6.3156630   2.3873689
## MAP4       4.2691385   1.6612717
## ANP32B     7.3917211   3.0901031
## PALLD      3.2582446   1.1595520
## CCND1     12.8155896   4.2152080
## PPP1R7     1.3771064   0.4559037
## ANXA4      0.9910171   0.3119008
## PSMC1      1.8565817   0.6670085
## RPL22     18.0802385  13.6614206
## CHMP5      2.2475471   0.8133687
## TRAK2      0.6266629   0.2023215
## TSR2       0.7283677   0.2514674
## CCT8       2.7170538   1.0197912
## TALDO1     4.1011196   1.4744413
## PKM       11.2169466   4.5918950
## TCEAL4     3.1529698   1.2502213
## GLRX3      2.7711079   1.0939891
## NPM1      23.0252024   9.4687059
## GSTO1      6.4090672   2.6387276
## RPL38     19.6448397  15.0090821
## RHOA      11.7100164   5.2632229
## ACTG1     58.3299147  24.2284448
## TPM1      48.2247502  19.5171008
## ETFA       1.4864417   0.6067108
## PINK1      0.8864088   0.3485708
## GLO1       2.1721765   0.8808620
## SDHC       2.8869098   1.1868481
## CALM2     14.6674950  11.1754578
## SDCBP      1.9522782   0.7591412
## ACOT7      1.0220068   0.3728179
## XRCC6      2.4669845   0.9961482
## ARPC3      8.9488207   3.8317064
## MOCS2      1.6057052   0.6131904
## COX8A      9.5675354   7.0774526
## CCT7       2.1654347   0.8407693
## PSME1      1.4480834   0.5684054
## ANXA6      1.8662255   0.6990283
## COPS6      2.9099862   1.1948019
## GAPDH     78.6747297  35.5773008
## HNRNPH3    2.5323273   1.0065451
## CSRP1      4.4190642   1.7509797
## COPS8      1.6976593   0.6760533
## ALDOA     15.4232089   6.8643521
## HINT1     15.6863038  11.2673292
## FAU       19.6744245  14.0563802
## ARPC4      2.9015761   1.2551251
## GHITM      3.0328364   1.2742042
## SCP2       2.2556397   0.9569698
## PSMB3      4.0481388   1.6106892
## TCEB2     10.1717989   7.4572456
## NDUFB6     2.6537542   1.1506787
## UQCRC2     1.3804937   0.5331099
## PRPS1      1.3683550   0.4798471
## ATP5H      5.4960878   2.3390760
## HTATSF1    1.1708382   0.4638847
## VBP1       1.6022892   0.6386328
## ENO1      14.8790232   6.7066811
## CRYAB     18.9404799   7.3762204
## YWHAQ      6.4686375   2.9145156
## PSMC3IP    0.8877453   0.3202799
## ZEB1       1.5141888   0.5936900
## MINOS1     3.9176994   2.8091867
## RPS26     14.6821112  10.8973177
## EIF4A1    11.3225181   4.8392496
## PSMC4      1.2766637   0.4702430
## HADHB      0.9749347   0.3807320
## PSMD2      3.6985492   1.5547875
## TMSB10   153.4991029 113.1099784
## KIF5B      4.7131726   2.1322704
## UQCRH      9.6206952   6.8209649
## CMPK1      2.1472764   0.8930390
## ARL1       1.4842055   0.5912341
## EIF3I      4.0479870   1.7472347
## EDF1       7.3976771   5.2080483
## S100A11   43.0101188  18.9626109
## PRDX6      5.9363655   2.5672280
## ESD        2.3907364   0.9864991
## HNRNPA3    4.9709106   2.2471915